Merge branch 'maint/2.5.x'

Author: effigies

Diff for: .zenodo.json

@@ -87,6 +87,11 @@
     {
       "name": "Moloney, Brendan"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Goncalves, Mathias",
+      "orcid": "0000-0002-7252-7771"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -130,11 +135,6 @@
     {
       "name": "Baker, Eric M."
     },
-    {
-      "affiliation": "MIT",
-      "name": "Goncalves, Mathias",
-      "orcid": "0000-0002-7252-7771"
-    },
     {
       "name": "Hayashi, Soichi"
     },
@@ -244,6 +244,11 @@
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
       "orcid": "0000-0001-9090-3024"
     },
+    {
+      "affiliation": "Center for Magnetic Resonance Research, University of Minnesota",
+      "name": "Braun, Henry",
+      "orcid": "0000-0001-7003-9822"
+    },
     {
       "name": "Solovey, Igor"
     },

Diff for: Changelog

@@ -25,6 +25,33 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
+2.5.1 (Monday 23 September 2019)
+================================
+
+Enhancements
+------------
+* Ignore endianness in ``nib-diff`` if values match (pr/799) (YOH, reviewed
+  by CM)
+
+Bug fixes
+---------
+* Correctly handle Philips DICOMs w/ derived volume (pr/795) (Mathias
+  Goncalves, reviewed by CM)
+* Raise CSA tag limit to 1000, parametrize for future relaxing (pr/798,
+  backported to 2.5.x in pr/800) (Henry Braun, reviewed by CM, MB)
+* Coerce data types to match NIfTI intent codes when writing GIFTI data
+  arrays (pr/806) (CM, reported by Tom Holroyd)
+
+Maintenance
+-----------
+* Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes
+  in Minc2 data (pr/804) (CM, reviewed by YOH)
+
+API changes and deprecations
+----------------------------
+* Deprecate ``nicom.dicomwrappers.Wrapper.get_affine()`` in favor of ``affine``
+  property; final removal in nibabel 4.0 (pr/796) (YOH, reviewed by CM)
+
 2.5.0 (Sunday 4 August 2019)
 ============================
 

Diff for: doc/source/index.rst

@@ -98,6 +98,7 @@ contributed code and discussion (in rough order of appearance):
 * Matt Cieslak
 * Egor Pafilov
 * Jath Palasubramaniam
+* Henry Braun
 
 License reprise
 ===============

Diff for: nibabel/gifti/gifti.py

@@ -264,16 +264,21 @@ def _to_xml_element(self):
     return DataTag(dataarray, encoding, datatype, ordering).to_xml()
 
 
-def _data_tag_element(dataarray, encoding, datatype, ordering):
+def _data_tag_element(dataarray, encoding, dtype, ordering):
     """ Creates data tag with given `encoding`, returns as XML element
     """
     import zlib
-    ord = array_index_order_codes.npcode[ordering]
+    order = array_index_order_codes.npcode[ordering]
     enclabel = gifti_encoding_codes.label[encoding]
     if enclabel == 'ASCII':
-        da = _arr2txt(dataarray, datatype)
+        # XXX Accommodating data_tag API
+        # On removal (nibabel 4.0) drop str case
+        da = _arr2txt(dataarray, dtype if isinstance(dtype, str) else KIND2FMT[dtype.kind])
     elif enclabel in ('B64BIN', 'B64GZ'):
-        out = dataarray.tostring(ord)
+        # XXX Accommodating data_tag API - don't try to fix dtype
+        if isinstance(dtype, str):
+            dtype = dataarray.dtype
+        out = np.asanyarray(dataarray, dtype).tostring(order)
         if enclabel == 'B64GZ':
             out = zlib.compress(out)
         da = base64.b64encode(out).decode()
@@ -456,11 +461,10 @@ def _to_xml_element(self):
         if self.coordsys is not None:
             data_array.append(self.coordsys._to_xml_element())
         # write data array depending on the encoding
-        dt_kind = data_type_codes.dtype[self.datatype].kind
         data_array.append(
             _data_tag_element(self.data,
                               gifti_encoding_codes.specs[self.encoding],
-                              KIND2FMT[dt_kind],
+                              data_type_codes.dtype[self.datatype],
                               self.ind_ord))
 
         return data_array

Diff for: nibabel/gifti/tests/test_gifti.py

@@ -20,6 +20,7 @@
 from nibabel.testing import clear_and_catch_warnings
 from .test_parse_gifti_fast import (DATA_FILE1, DATA_FILE2, DATA_FILE3,
                                     DATA_FILE4, DATA_FILE5, DATA_FILE6)
+import itertools
 
 
 def test_gifti_image():
@@ -399,3 +400,20 @@ def test_data_array_round_trip():
     gio = GiftiImage.from_file_map(fmap)
     vertices = gio.darrays[0].data
     assert_array_equal(vertices, verts)
+
+
+def test_darray_dtype_coercion_failures():
+    dtypes = (np.uint8, np.int32, np.int64, np.float32, np.float64)
+    encodings = ('ASCII', 'B64BIN', 'B64GZ')
+    for data_dtype, darray_dtype, encoding in itertools.product(dtypes,
+                                                                dtypes,
+                                                                encodings):
+        da = GiftiDataArray(np.arange(10).astype(data_dtype),
+                            encoding=encoding,
+                            intent='NIFTI_INTENT_NODE_INDEX',
+                            datatype=darray_dtype)
+        gii = GiftiImage(darrays=[da])
+        gii_copy = GiftiImage.from_bytes(gii.to_bytes())
+        da_copy = gii_copy.darrays[0]
+        assert_equal(np.dtype(da_copy.data.dtype), np.dtype(darray_dtype))
+        assert_array_equal(da_copy.data, da.data)

Diff for: nibabel/nicom/dicomwrappers.py

@@ -22,6 +22,7 @@
 from ..openers import ImageOpener
 from ..onetime import setattr_on_read as one_time
 from ..pydicom_compat import tag_for_keyword, Sequence
+from ..deprecated import deprecate_with_version
 
 
 class WrapperError(Exception):
@@ -94,7 +95,7 @@ class Wrapper(object):
 
     Methods:
 
-    * get_affine()
+    * get_affine() (deprecated, use affine property instead)
     * get_data()
     * get_pixel_array()
     * is_same_series(other)
@@ -103,6 +104,7 @@ class Wrapper(object):
 
     Attributes and things that look like attributes:
 
+    * affine : (4, 4) array
     * dcm_data : object
     * image_shape : tuple
     * image_orient_patient : (3,2) array
@@ -285,18 +287,19 @@ def get(self, key, default=None):
         """ Get values from underlying dicom data """
         return self.dcm_data.get(key, default)
 
+    @deprecate_with_version('get_affine method is deprecated.\n'
+                            'Please use the ``img.affine`` property '
+                            'instead.',
+                            '2.5.1', '4.0')
     def get_affine(self):
-        """ Return mapping between voxel and DICOM coordinate system
+        return self.affine
 
-        Parameters
-        ----------
-        None
+    @property
+    def affine(self):
+        """ Mapping between voxel and DICOM coordinate system
 
-        Returns
-        -------
-        aff : (4,4) affine
-           Affine giving transformation between voxels in data array and
-           mm in the DICOM patient coordinate system.
+        (4, 4) affine matrix giving transformation between voxels in data array
+        and mm in the DICOM patient coordinate system.
         """
         # rotation matrix already accounts for the ij transpose in the
         # DICOM image orientation patient transform.  So. column 0 is

Diff for: setup.cfg

@@ -31,7 +31,7 @@ python_requires = >=3.5.1
 install_requires =
     numpy >=1.12
 tests_require =
-    nose >=0.10.1
+    nose >=0.11
     mock
 test_suite = nose.collector
 zip_safe = False
@@ -52,7 +52,7 @@ style =
 test =
     coverage
     mock
-    nose >=0.10.1
+    nose >=0.11
 all =
     %(dicom)s
     %(doc)s